The relatively flat ride didn't cause any major changes at the top of the overall classification.
Nibali lost two seconds of his lead, seeing it reduced to 31 seconds over Nicolas Roche. Alejandro Valverde and Christopher Horner are tied for third overall at 46 seconds behind.
Friday's 13th stage remains in the northeastern region of Catalonia for a second straight transition stage, a 169-kilometer (105-mile) route from Valls to Castelldefels.
The three-week race then heads back into the mountains for a trilogy of stages in the Pyrenees that could prove decisive.
After losing time in Wednesday's individual time trial, Joaquim Rodriguez said he needs to attack in the mountains to have a chance, as he's already 2 minutes, 33 seconds off Nibali's pace.
"It's clear I am not having my best race," said Rodriguez. "I hope that the motivation of riding at home helps me. To come back I will have to shake the race up."
The 68th Vuelta ends in Madrid on Sept. 15.